Feature/annotator plugin#5

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braswent wants to merge 302 commits intostevencox:mainfrom

helxplatform:feature/annotator-plugin

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Commits on Feb 9, 2021

Commits on Feb 11, 2021

Adding prerequisite secretes and volume
YaphetKG
committed

Commits on Feb 16, 2021

Adding prerequisite secretes and volume to read me , some instructions for easier run of roger helm chart.
YaphetKG
committed

Commits on Mar 5, 2021

Indexing and integration (#9)
YaphetKG
authored

Commits on Mar 10, 2021

Config overhaul (#10)
YaphetKG
authored

Commits on Mar 19, 2021

Commits on Mar 23, 2021

Indexing and validation, adds validation , reincorporates dug index vars (#13)
YaphetKG
authored

Commits on Mar 24, 2021

Commits on Mar 25, 2021

Commits on Apr 8, 2021

Feature/makefiles and cli (#17)
YaphetKG
authored

Commits on Apr 19, 2021

Enabling docker compose for local development
Carl Schreep
committed

Commits on Apr 20, 2021

Improving Makefile to bring up stack more easily
Carl Schreep
committed
Makefile now runs tests
Carl Schreep
committed
Merge branch 'develop' of github.com:helxplatform/roger into feature/cicd-improvements
Carl Schreep
committed
Adding pytest to requirements. Putting mock definitions in conftest
Carl Schreep
committed
Jenkinsfile. Skipping tests that aren't working yet
Carl Schreep
committed

Commits on Apr 23, 2021

Unzip dbgap and index, no kgx for dbgap yet (#19)

YaphetKG
and
Carl Schreep
authored
Update requirements.txt
YaphetKG
authored
Update core.py
YaphetKG
authored

Commits on Apr 26, 2021

moving dag_util to roger module
Carl Schreep
committed
Bumping version
Carl Schreep
committed
Merge branch 'develop' of github.com:helxplatform/roger into feature/cicd-improvements
Carl Schreep
committed
input files path
Carl Schreep
committed
Logging line numbers
Carl Schreep
committed
Logging to find exceptions
Carl Schreep
committed
More logging
Carl Schreep
committed

Commits on Apr 27, 2021

Adding ability to configure data output dir via env var
Carl Schreep
committed
Error handling and logging for db gap files
Carl Schreep
committed
Redis config from env vars
Carl Schreep
committed
tranql connection info from env vars
Carl Schreep
committed
redis graph variables
Carl Schreep
committed
db_gap file pathing issue
Carl Schreep
committed
annotate files can handle plugins correctly
Carl Schreep
committed
parser call
Carl Schreep
committed

Commits on Apr 28, 2021

Merge pull request #20 from helxplatform/release/0.1.0
cschreep
authored
Redis configs in validate
Carl Schreep
committed

Commits on May 6, 2021

Pulling tranql endpoint from environment
Carl Schreep
committed

Commits on May 10, 2021

Adding Configuration classes, integrating Dug changes
Carl Schreep
committed

Commits on May 11, 2021

Removing some debug statements. Fixing test
Carl Schreep
committed

Commits on May 17, 2021

Pinning dug dependency
Carl Schreep
committed
Merge pull request #21 from helxplatform/feature/cicd-improvements
cschreep
authored

Commits on May 24, 2021

Adding unit tests to make test target
Carl Schreep
committed

Commits on May 26, 2021

Feature/dbgap data dicts (#18)

YaphetKG
and
Carl Schreep
authored

Commits on Jun 2, 2021

Updating dag to fetch data from network rather than expect it on disk
Carl Schreep
committed
Jenkinsfile
Carl Schreep
committed
Merge branch 'develop' into feature/network-data-sources
Carl Schreep
committed

Commits on Jun 8, 2021

Merge pull request #22 from helxplatform/feature/network-data-sources
cschreep
authored

Commits on Jun 10, 2021

Updating dug dependency to 2.2.0
Carl Schreep
committed
Merge pull request #23 from helxplatform/feature/update-dug
cschreep
authored

Commits on Jun 11, 2021

Volume name
Carl Schreep
committed
Commenting out volume mounts
Carl Schreep
committed
return values for file fetch
Carl Schreep
committed
normalizer service endpoint
Carl Schreep
committed

Commits on Jun 22, 2021

Merge pull request #24 from helxplatform/fix/pvc-name
cschreep
authored

Commits on Jun 24, 2021

Fix/indexing concepts tweak (#25)
YaphetKG
authored

Commits on Jun 25, 2021

reverts download url (#26)

YaphetKG
and
yaphetkg
authored

Commits on Jun 28, 2021

Feature/new kgx files (#27)

YaphetKG
and
yaphetkg
authored

Commits on Jul 8, 2021

Bumping version
Carl Schreep
committed
Bumping version
Carl Schreep
committed
Merge pull request #28 from helxplatform/release/0.3.0
cschreep
authored
Bumping version
Carl Schreep
committed

Commits on Jul 12, 2021

Updating dug dependency to 2.3.0
Carl Schreep
committed
Merge pull request #29 from helxplatform/feature/dug-2.3
cschreep
authored

Commits on Jul 22, 2021

Commits on Jul 23, 2021

Commits on Jul 26, 2021

Commits on Jul 29, 2021

Commits on Aug 4, 2021

adding support multi-tenancy of datasets
YaphetKG
committed

Commits on Aug 16, 2021

fix tests
Yaphetkg
committed

Commits on Aug 18, 2021

Merge pull request #30 from helxplatform/feature/nidaW1
cschreep
authored
Bumping version
Carl Schreep
committed
Pinning Dug dep
Carl Schreep
committed
Merge branch 'main' into release/0.4
cschreep
authored
Merge branch 'develop' of github.com:helxplatform/roger into release/0.4
Carl Schreep
committed
Merge branch 'release/0.4' of github.com:helxplatform/roger into release/0.4
Carl Schreep
committed
Fixing dug version pin
Carl Schreep
committed

Commits on Aug 19, 2021

Pinning Dug to released version
Carl Schreep
committed
Merge pull request #31 from helxplatform/release/0.4
cschreep
authored
Bumping version
Carl Schreep
committed
Bumping version
Carl Schreep
committed

Commits on Sep 20, 2021

Feature/biolink 2.1 (#34)

authored

Commits on Sep 21, 2021

Bumping version
Carl Schreep
committed
Merge pull request #36 from helxplatform/release/0.5
cschreep
authored
Bumping version
Carl Schreep
committed
Bumping version
Carl Schreep
committed

Commits on Sep 28, 2021

Commits on Oct 7, 2021

Commits on Oct 8, 2021

Feature/caching overhaul (#38)
YaphetKG
authored

Commits on Oct 12, 2021

Adding S3 Utils and Config classes. Implementing S3 to fetch data from bucket instead of web.
Carl Schreep
committed

Commits on Oct 13, 2021

Fixing import; updating requirements
Carl Schreep
committed
Import paths and module name
Carl Schreep
committed
Import path
Carl Schreep
committed

Commits on Oct 15, 2021

Merge pull request #41 from helxplatform/feature/nidaW2squash
warrenstephens
authored

Commits on Oct 18, 2021

Merge branch 'develop' of github.com:helxplatform/roger into feature/s3-utils-simple
Carl Schreep
committed
Updating NIDA task to use S3
Carl Schreep
committed
Update requirements.txt
YaphetKG
authored
Merge pull request #42 from helxplatform/dug-lib-update
cschreep
authored
Merge branch 'develop' of github.com:helxplatform/roger into feature/s3-utils-simple
Carl Schreep
committed
Release/0.6.0 (#43)

authored
Making sure dags are backwards-compatible
Carl Schreep
committed
Dug utils
Carl Schreep
committed
Logic for data set matching
Carl Schreep
committed

Commits on Oct 19, 2021

File info for s3/stars
Carl Schreep
committed
Logic for specifying data source
Carl Schreep
committed
Merge pull request #40 from helxplatform/feature/s3-utils-simple
cschreep
authored

Commits on Oct 20, 2021

Initial pass at adding SPARC processor
Carl Schreep
committed
sparc metadata
Carl Schreep
committed
Logging
Carl Schreep
committed
tmp making SciCrunchParser init explicit
Carl Schreep
committed
Undoing previous commit
Carl Schreep
committed

Commits on Oct 21, 2021

scicrunch parser name
Carl Schreep
committed
scicrunch parser name
Carl Schreep
committed
Makefile
Carl Schreep
committed

Commits on Nov 2, 2021

Batching key delete using scan (#45)

YaphetKG
and
Yaphetkg
authored

Commits on Nov 3, 2021

Bumping version
Carl Schreep
committed

Commits on Nov 5, 2021

Merge pull request #44 from helxplatform/feature/sparc-1.0-data
cschreep
authored

Commits on Nov 8, 2021

Patch/delete keys (#46)

YaphetKG
and
Yaphetkg
authored
adding some logging
Yaphetkg
committed

Commits on Nov 9, 2021

Feature/redis lib updates (#47)

YaphetKG
and
Yaphetkg
authored

Commits on Nov 11, 2021

Commits on Nov 29, 2021

Changing normalizer URL
Carl Schreep
committed
Pinning dug version to 2.7.rc0
Carl Schreep
committed
Bumping version
Carl Schreep
committed

Commits on Nov 30, 2021

Pathing for sparc data
Carl Schreep
committed

Commits on Dec 2, 2021

Bumping dug to released versioN
Carl Schreep
committed
Merge branch 'main' of github.com:helxplatform/roger into release/0.7.rc0
Carl Schreep
committed
Merge pull request #49 from helxplatform/release/0.7.rc0
cschreep
authored
Bumping version
Carl Schreep
committed
Bumping version
Carl Schreep
committed

Commits on Feb 9, 2022

Feature/cde crawls (#51)

YaphetKG
and
Yaphetkg
authored

Commits on Feb 10, 2022

Remove logging of config; contains redis and S3 keys (#52)
mac-chaffee
authored

Commits on Feb 11, 2022

when two graph sets are downloaded, bug that deletes the first download (#53)

YaphetKG
and
Yaphetkg
authored

Commits on Apr 1, 2022

added the version and the new tag
HowardLander
committed

Commits on Apr 4, 2022

Commits on Apr 5, 2022

Cde harmonization 2 (#57)

YaphetKG
and
Yaphetkg
authored

Commits on Apr 8, 2022

Merge branch 'sparc_parser_fix' into develop
HowardLander
authored

Commits on Apr 19, 2022

Commits on Apr 22, 2022

Update _version.py
YaphetKG
authored

Commits on May 3, 2022

Anvil pipeline (#60)

YaphetKG
and
Yaphetkg
authored

Commits on May 24, 2022

Merge pull request #61 from helxplatform/new-jenkins-test
Hoid
authored

Commits on Jun 9, 2022

Commits on Jun 29, 2022

Add versioning and tagging for develop and master + bump version.
cnbennett3
committed

Commits on Jul 1, 2022

Merge pull request #62 from helxplatform/jenkins-test
cnbennett3
authored

Commits on Jul 13, 2022

Commits on Jul 18, 2022

Commits on Aug 25, 2022

Ncpi datasets (#64)
YaphetKG
authored

Commits on Oct 5, 2022

Sprint task (#65)

YaphetKG
and
Yaphetkg
authored

Commits on Jan 5, 2023

Bacpac parsing (#66)

authored

Commits on Jan 26, 2023

Issue 124 annotation kgx (#69)

authored

Commits on Jul 19, 2023

Commits on Jul 26, 2023

Filerenames. Deprecated DummyOperator -> EmptyOperator, imports. (#74)
vladimir2217
authored

Commits on Aug 15, 2023

Changes to fix the loading bug for json files (#77)
HowardLander
authored

Commits on Aug 16, 2023

Commits on Aug 18, 2023

Commits on Aug 23, 2023

Commits on Aug 24, 2023

Study names plus (#79)
YaphetKG
authored

Commits on Sep 6, 2023

Mds import (#82)
YaphetKG
authored

Commits on Sep 29, 2023

Bacpac and cde (#83)
YaphetKG
authored

Commits on Oct 5, 2023

Commits on Oct 31, 2023

Commits on Nov 6, 2023

Annotator plugin on develop branch
braswent
committed

Commits on Jan 4, 2024

Update __init__.py
braswent
authored